Draft Genome Sequence of the Biocontrol and Plant Growth-Promoting Rhizobacterium Pseudomonas fluorescens strain UM270
© Hernández-Salmerón et al. 2015
Received: 27 May 2015
Accepted: 9 September 2015
Published: 13 January 2016
The Pseudomonas fluorescens strain UM270 was isolated form the rhizosphere of wild Medicago spp. A previous work has shown that this pseudomonad isolate was able to produce diverse diffusible and volatile compounds involved in plant protection and growth promotion. Here, we present the draft genome sequence of the rhizobacterium P. fluorescens strain UM270. The sequence covers 6,047,974 bp of a single chromosome, with 62.66 % G + C content and no plasmids. Genome annotations predicted 5,509 genes, 5,396 coding genes, 59 RNA genes and 110 pseudogenes. Genome sequence analysis revealed the presence of genes involved in biological control and plant-growth promoting activities. We anticipate that the P. fluorescens strain UM270 genome will contribute insights about bacterial plant protection and beneficial properties through genomic comparisons among fluorescent pseudomonads.
KeywordsPseudomonas fluorescens Biocontrol PGPR
Plant pathogens cause diverse crop plant diseases resulting in drastic economic losses around the world. An alternative to the use of chemicals to control plant pathogens is the employment of eco-friendly bacterial agents [1, 2]. An ideal bacterial biocontrol agent would be one with the additional capacity to directly stimulate plant growth . Here, we report the draft genome sequence of the novel strain Pseudomonas fluorescens strain UM270. This strain was previously isolated and characterized for its excellent capacities for biocontrol of phytopathogens and plant growth promotion .
In a previous report, our group showed that the P. fluorescens strain UM270, among other three pseudomonad strains, was the best in promoting the growth of Medicago truncatula Gaertn. plants by significantly increasing biomass and chlorophyll content. During confrontation assays, strain UM270 inhibited the growth of agro-economically important fungal phytopathogens such as Botrytis cinerea , Rhizoctonia solani , Diaporthe phaseolorum , and Colletotrichum lindemuthianum . In biocontrol experiments, the strain UM270 protected M. truncatula plants from B. cinerea infection, reducing general stem disease symptoms, root browning and necrosis .
Importantly, the strain UM270 exerted these activities through the emission of either diffusible compounds (such as phenazines, cyanogens, 1-aminocyclopropane-1-carboxylate deaminase, siderophores, proteases and indole-3-acetic acid) or volatiles (like dimethyl disulfide and dimethylhexadecylamine) , revealing that the strain UM270 contains direct and indirect mechanisms to promote plant growth .
Classification and features
Classification and general features of Pseudomonas fluorescens strain UM270
Species Pseudomonas fluorescens
pH range; Optimum
NaCl 1-4 %
Medicago spp. root associated
19° 46’ 6” N
101° 11’ 22” W
Genome sequencing information
Genome project history
High-quality draft (Full genome representation)
3 libraries of 400–450 bp, 600 bp and 1,000 bp.
Newbler v. 2.9
Gene calling method
NCBI Prokaryotic Genome, Annotation Pipeline
GenBank Date of Release
Source Material Identifier
Agriculture, Plant-Bacteria Interaction, Biocontrol
Growth conditions and genomic DNA preparation
From a single colony culture the P. fluorescens strain UM270 was inoculated on 50 ml of King’s B medium , grown overnight at 28 °C with in agitation (250 rpm). One milliliter of the culture was serially diluted to be analyzed further. We confirmed the morphology and antibiotic-resistance phenotype of the strain. From the culture, 20 ml were taken to isolate the genomic DNA by using the Wizard® Genomic DNA Purification Kit following manufacture’s instructions (Promega). DNA samples were subjected to an additional purification step with the same Wizard® Genomic DNA Purification Kit (Promega). The quality and quantity of the final DNA sample were evaluated by agarose gel electrophoresis and by using a NanoDrop 1000 Spectrophotometer (Thermo Scientific).
Genome sequencing and assembly
Genomic DNA samples of P. fluorescens strain UM270 were sent to a sequencing service at the LANGEBIO-Irapuato, México. Genome sequencing was performed using a MiSeq Sequencer (Illumina, Inc.) generating three paired-end libraries (400–450 bp, 600 bp and 1,000 bp, respectively) with a coverage of approximately 45×. The P. fluorescens strain UM270 draft genome we ran a blastn comparison using the contigs as query, against the genome sequence of P. fluorescens Pf0-1 as target reference. To order the contigs we followed the matching coordinates of the reference genome. Project information is shown in Table 2.
Genome annotation was carried out with RAST  and the Prokaryotic Genome Annotation Pipeline tools . Statistics for the genome assembly were calculated using software Newbler v2.9 (Roche) and are shown in Table 2. This Whole Genome Shotgun sequence project has been deposited at DDBJ/EMBL/GenBank under accession JXNZ00000000. The version described in this paper is version JXNZ00000000.
% of total
Genome size (bp)
DNA coding (bp)
DNA G + C (bp)
Protein coding genes
Genes in internal clusters
Genes with function prediction
Genes assigned to COGs
Genes with Pfam domains
Genes with signal peptides
Genes with transmembrane helices
Number of genes associated with the 25 general COG functional categories
% of totala
Translation, ribosomal structure and biogenesis
RNA processing and modification
Replication, recombination and repair
Chromatin structure and dynamics
Cell cycle control, cell division, chromosome partitioning
Signal transduction mechanisms
Cell wall/membrane biogenesis
Intracellular trafficking and secretion
Posttranslational modification, protein turnover, chaperones
Energy production and conversion
Carbohydrate transport and metabolism
Amino acid transport and metabolism
Nucleotide transport and metabolism
Coenzyme transport and metabolism
Lipid transport and metabolism
Inorganic ion transport and metabolism
Secondary metabolites biosynthesis, transport and catabolism
General function prediction only
Not in COGs
Insights from the genome sequence
The draft genome sequence reported here covers its full genome and at first analysis reveals the presence of multiple genes participating in the synthesis of diffusible metabolites and volatile organic compounds produced by P. fluorescens strain UM270. Some of this antimicrobial arsenal includes compounds like phenazine (phzFABCD), pyocyanin (pcnCDE), pyoverdine (pvdPD), 2,4-diacetylphloroglucinol (phlACBD) and the volatile hydrogen cyanide (hcnCB), important for the biological control of several plant diseases caused by phytopathogenic fungi, oomycetes, and bacteria . Other plant-bacteria communication genes detected in the strain UM270 genome are acdS and iaaMH, encoding for an ACC deaminase (1-aminocyclopropane-1-carboxylate) protein and IAA (indole-3-acetic acid) biosynthesis. The synergistic interaction of ACC deaminase and both plant and bacterial auxin, IAA, is relevant for the optimal functioning of PGPR to directly promote plant growth and also protect plants against environmental stresses, and bacterial and fungal pathogens . Other genes such as pcdQ, which codes for an Acyl-homoserine lactone acylase, important for bacterial communication and biofilm formation, were detected, as well as Secretion Systems Type II to VI and orthologs of the toxin-antitoxin loci vapBC-1 and vapXD. These last determinants are important for survival, competence and colonization of the rhizosphere and root systems .
The strain UM270 was selected for genome sequencing due to its biocontrol and plant growth promoting properties . The plant beneficial mechanisms exerted by this rhizobacterium involved direct and indirect mechanisms. Here, the draft genome sequence of the P. fluorescens strain UM270 revealed further genetic elements involved in plant-bacterial communication, as well as in rhizosphere competence and colonization. We anticipate that the genome of P. fluorescens strain UM270 will contribute to new insights about biocontrol and plant beneficial activities through genomic comparisons among available complete genomes of pseudomonad strains.
We thank CONACYT-México (Project Number: 169346) and CIC-UMSNH (2014–2015) for financial support to our research projects. JEH-S and RH-L received scholarships from CONACYT-México. JEH-S acknowledges a scholarship from the Government of Canada under The Emerging Leaders in the Americas Program (ELAP). This paper is a requirement to obtain the Ph.D. of JEH-S.
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